On 10/18/11 1:57 PM, Maggie Pruitt wrote: > I am interested in using Modeller for predicting the structure of the G > protein-coupled receptor I study. This protein does not have any > homologous proteins in the PDB database and there is no experimental > data to help model the protein. Knowing this, can Modeller provide an > accurate structure of my protein to use in molecular dynamics > simulations? I understand that I can choose other crystallized GPCRs to > use as templates, but I am concerned that since Modeller is a homology > modeling program that the end model would simply look like my protein > forced onto the template structure.
Yes, you are exactly correct. Modeller is not limited to using homologs as templates; it can use any protein that you believe is structurally similar to the protein you intend to model. But if you choose a template that is not similar, you will likely get a poor model.
Ben Webb, Modeller Caretaker